Atomistry » Magnesium » PDB 5a28-5aby » 5a94
Atomistry »
  Magnesium »
    PDB 5a28-5aby »
      5a94 »

Magnesium in PDB 5a94: Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1

Enzymatic activity of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1

All present enzymatic activity of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1:
3.2.1.73;

Protein crystallography data

The structure of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1, PDB code: 5a94 was solved by G.Sulzenbacher, M.Lafond, T.Freyd, B.Henrissat, R.M.Coutinho, J.G.Berrin, M.L.Garron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.42 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 188.643, 132.753, 131.352, 90.00, 133.78, 90.00
R / Rfree (%) 17.9 / 19

Other elements in 5a94:

The structure of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 (pdb code 5a94). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1, PDB code: 5a94:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5a94

Go back to Magnesium Binding Sites List in 5a94
Magnesium binding site 1 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:24.6
occ:1.00
 O A:HOH2162 2.2 23.6 1.0
O A:VAL178 2.2 21.6 1.0
O A:VAL181 2.2 20.0 1.0
O A:HOH2158 2.4 21.9 1.0
O A:HOH2159 2.5 25.9 1.0
C A:VAL178 3.3 22.6 1.0
C A:VAL181 3.3 19.9 1.0
CB A:VAL181 3.9 20.2 1.0
CA A:VAL181 4.0 20.3 1.0
N A:VAL178 4.0 22.9 1.0
CA A:VAL178 4.1 22.4 1.0
N A:VAL181 4.1 20.1 1.0
O A:TYR175 4.2 18.5 1.0
CG1 A:VAL223 4.2 24.4 1.0
N A:PRO179 4.3 22.8 1.0
CA A:PRO179 4.3 21.5 1.0
N A:ALA182 4.4 19.8 1.0
CB A:VAL178 4.4 21.3 1.0
C A:PRO179 4.5 20.9 1.0
O A:PRO179 4.5 20.9 1.0
CE1 A:PHE50 4.6 23.9 1.0
CG1 A:VAL181 4.6 20.1 1.0
OG1 A:THR222 4.7 24.2 1.0
CA A:ALA182 4.7 19.5 1.0
OD2 A:ASP220 4.7 21.4 1.0
O A:HOH2025 4.8 20.9 1.0
O A:HOH2026 4.8 22.7 1.0
OH A:TYR184 4.8 21.8 1.0
CA A:VAL223 5.0 23.4 1.0
CD1 A:PHE50 5.0 23.4 1.0
CB A:VAL223 5.0 23.6 1.0

Magnesium binding site 2 out of 6 in 5a94

Go back to Magnesium Binding Sites List in 5a94
Magnesium binding site 2 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:25.9
occ:1.00
 O B:HOH2134 2.1 21.3 1.0
O B:HOH2138 2.3 22.0 1.0
O B:VAL181 2.3 20.1 1.0
O B:VAL178 2.4 23.8 1.0
O B:HOH2133 2.5 24.3 1.0
C B:VAL178 3.4 23.8 1.0
C B:VAL181 3.5 18.9 1.0
CG1 B:VAL223 4.0 23.6 1.0
CB B:VAL181 4.1 20.4 1.0
N B:VAL178 4.1 24.2 1.0
CA B:VAL181 4.2 20.1 1.0
O B:TYR175 4.3 20.5 1.0
CA B:VAL178 4.3 23.7 1.0
N B:VAL181 4.3 20.4 1.0
N B:PRO179 4.4 24.3 1.0
OG1 B:THR222 4.4 27.3 1.0
CA B:PRO179 4.4 24.1 1.0
CE1 B:PHE50 4.5 24.1 1.0
N B:ALA182 4.5 18.6 1.0
OD2 B:ASP220 4.5 22.6 1.0
CB B:VAL178 4.6 23.2 1.0
C B:PRO179 4.6 23.3 1.0
O B:PRO179 4.6 23.9 1.0
O B:HOH2021 4.6 24.8 1.0
CG1 B:VAL181 4.7 20.4 1.0
CA B:ALA182 4.7 18.3 1.0
CA B:VAL223 4.8 22.4 1.0
CB B:VAL223 4.8 22.8 1.0
OH B:TYR184 4.8 20.4 1.0
CD1 B:PHE50 4.9 24.4 1.0
O B:THR222 4.9 26.2 1.0
O B:HOH2020 4.9 18.8 1.0

Magnesium binding site 3 out of 6 in 5a94

Go back to Magnesium Binding Sites List in 5a94
Magnesium binding site 3 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:26.2
occ:1.00
 O C:VAL178 2.2 19.0 1.0
O C:HOH2134 2.2 22.9 1.0
O C:VAL181 2.3 19.7 1.0
O C:HOH2140 2.4 27.0 1.0
O C:HOH2137 2.5 24.2 1.0
C C:VAL178 3.3 20.4 1.0
C C:VAL181 3.5 19.4 1.0
CB C:VAL181 4.0 19.9 1.0
N C:VAL178 4.0 21.7 1.0
CA C:VAL178 4.1 20.5 1.0
CA C:VAL181 4.1 19.8 1.0
O C:TYR175 4.1 18.6 1.0
N C:VAL181 4.2 20.6 1.0
CG1 C:VAL223 4.2 25.9 1.0
N C:PRO179 4.3 20.5 1.0
CA C:PRO179 4.3 21.0 1.0
CB C:VAL178 4.4 20.6 1.0
C C:PRO179 4.5 20.7 1.0
CE1 C:PHE50 4.5 23.9 1.0
N C:ALA182 4.5 18.9 1.0
OD2 C:ASP220 4.6 22.4 1.0
OG1 C:THR222 4.6 23.9 1.0
O C:PRO179 4.6 21.2 1.0
CG1 C:VAL181 4.6 20.9 1.0
O C:HOH2029 4.7 24.9 1.0
CA C:ALA182 4.8 18.6 1.0
OH C:TYR184 4.8 20.1 1.0
CD1 C:PHE50 4.9 23.1 1.0
O C:HOH2028 5.0 27.1 1.0

Magnesium binding site 4 out of 6 in 5a94

Go back to Magnesium Binding Sites List in 5a94
Magnesium binding site 4 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:26.8
occ:1.00
 O D:HOH2104 2.1 30.0 1.0
O D:VAL178 2.2 29.0 1.0
O D:VAL181 2.3 26.1 1.0
O D:HOH2101 2.4 30.8 1.0
O D:HOH2100 2.7 20.4 1.0
C D:VAL178 3.3 30.2 1.0
C D:VAL181 3.4 25.6 1.0
CB D:VAL181 4.1 25.8 1.0
N D:VAL178 4.1 29.4 1.0
CA D:VAL181 4.1 25.6 1.0
CA D:VAL178 4.1 30.5 1.0
N D:VAL181 4.2 26.2 1.0
N D:PRO179 4.2 32.0 1.0
CA D:PRO179 4.2 30.8 1.0
CG1 D:VAL223 4.3 27.8 1.0
C D:PRO179 4.4 29.8 1.0
O D:TYR175 4.4 24.7 1.0
CE1 D:PHE50 4.4 33.4 1.0
N D:ALA182 4.4 25.1 1.0
O D:HOH2017 4.4 22.7 1.0
O D:PRO179 4.4 29.0 1.0
CB D:VAL178 4.5 30.4 1.0
OG1 D:THR222 4.5 31.5 1.0
O D:HOH2016 4.6 32.3 1.0
CA D:ALA182 4.6 24.8 1.0
CG1 D:VAL181 4.7 25.8 1.0
OD2 D:ASP220 4.7 32.2 1.0
CD1 D:PHE50 4.8 33.1 1.0
CA D:VAL223 4.9 27.6 1.0

Magnesium binding site 5 out of 6 in 5a94

Go back to Magnesium Binding Sites List in 5a94
Magnesium binding site 5 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:22.0
occ:1.00
 O E:HOH2149 2.1 20.9 1.0
O E:VAL178 2.3 17.8 1.0
O E:VAL181 2.3 18.3 1.0
O E:HOH2158 2.3 19.4 1.0
O E:HOH2152 2.5 22.6 1.0
C E:VAL178 3.4 19.5 1.0
C E:VAL181 3.5 16.9 1.0
CB E:VAL181 4.0 17.4 1.0
N E:VAL178 4.0 20.1 1.0
CG1 E:VAL223 4.0 23.9 1.0
CA E:VAL181 4.1 17.6 1.0
O E:TYR175 4.2 17.1 1.0
CA E:VAL178 4.2 19.2 1.0
N E:VAL181 4.2 17.9 1.0
N E:PRO179 4.4 18.4 1.0
CB E:VAL178 4.5 19.2 1.0
CA E:PRO179 4.5 18.8 1.0
OG1 E:THR222 4.5 22.9 1.0
OD2 E:ASP220 4.5 21.2 1.0
N E:ALA182 4.5 16.7 1.0
CE1 E:PHE50 4.6 20.9 1.0
CG1 E:VAL181 4.6 16.9 1.0
C E:PRO179 4.6 18.0 1.0
O E:PRO179 4.7 17.7 1.0
OH E:TYR184 4.7 15.9 1.0
CA E:ALA182 4.8 16.2 1.0
CA E:VAL223 4.9 21.6 1.0
CB E:VAL223 4.9 23.2 1.0
O E:HOH2033 4.9 18.0 1.0
O E:HOH2031 5.0 17.7 1.0
CD1 E:PHE50 5.0 20.9 1.0

Magnesium binding site 6 out of 6 in 5a94

Go back to Magnesium Binding Sites List in 5a94
Magnesium binding site 6 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:27.0
occ:1.00
 O F:VAL181 2.2 21.2 1.0
O F:VAL178 2.3 22.2 1.0
O F:HOH2113 2.4 31.5 1.0
O F:HOH2111 2.4 20.0 1.0
O F:HOH2115 2.5 26.6 1.0
C F:VAL181 3.3 20.7 1.0
C F:VAL178 3.4 22.6 1.0
CB F:VAL181 3.9 21.4 1.0
CA F:VAL181 4.0 21.3 1.0
N F:VAL178 4.1 23.5 1.0
N F:VAL181 4.2 21.9 1.0
CG1 F:VAL223 4.2 27.1 1.0
CA F:VAL178 4.2 22.7 1.0
O F:TYR175 4.3 23.6 1.0
N F:PRO179 4.3 22.7 1.0
CA F:PRO179 4.4 22.2 1.0
N F:ALA182 4.4 20.6 1.0
CB F:VAL178 4.5 22.3 1.0
C F:PRO179 4.5 21.8 1.0
O F:PRO179 4.5 21.7 1.0
CE1 F:PHE50 4.6 25.9 1.0
OG1 F:THR222 4.6 30.5 1.0
CG1 F:VAL181 4.6 22.4 1.0
CA F:ALA182 4.6 20.4 1.0
OD2 F:ASP220 4.7 25.2 1.0
O F:HOH2024 4.8 23.1 1.0
CA F:VAL223 4.8 25.9 1.0
OH F:TYR184 4.9 23.0 1.0
CB F:VAL223 4.9 26.3 1.0
CD1 F:PHE50 5.0 25.3 1.0

Reference:

M.Lafond, G.Sulzenbacher, T.Freyd, B.Henrissat, J.G.Berrin, M.L.Garron. The Quaternary Structure of A Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans J.Biol.Chem. V. 291 7183 2016.
ISSN: ISSN 0021-9258
PubMed: 26755730
DOI: 10.1074/JBC.M115.695999
Page generated: Sun Sep 29 00:21:18 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy